chr15-26178900-C-T

Position:

• chr15-26178900-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0381 in 151,876 control chromosomes in the GnomAD database, including 153 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.038 (153 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0382 AC: 5792 AN: 151758 Hom.: 153 Cov.: 31

Gnomad AFR AF: 0.0103

Gnomad AMI AF: 0.0793

Gnomad AMR AF: 0.0300

Gnomad ASJ AF: 0.0756

Gnomad EAS AF: 0.000390

Gnomad SAS AF: 0.0206

Gnomad FIN AF: 0.0380

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.0587

Gnomad OTH AF: 0.0373

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0381 AC: 5789 AN: 151876 Hom.: 153 Cov.: 31 AF XY: 0.0360 AC XY: 2675 AN XY: 74220

Gnomad4 AFR AF: 0.0102

Gnomad4 AMR AF: 0.0299

Gnomad4 ASJ AF: 0.0756

Gnomad4 EAS AF: 0.000391

Gnomad4 SAS AF: 0.0206

Gnomad4 FIN AF: 0.0380

Gnomad4 NFE AF: 0.0587

Gnomad4 OTH AF: 0.0369

Alfa AF: 0.0257 Hom.: 155

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.34
DANN	Benign	0.92

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs547843; hg19: chr15-26424047;